--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_filter_to_accession.py	Tue Jun 14 08:15:55 2022 +0000
@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""Return a filter fasta file for list of accession"""
+
+import argparse
+import sys
+
+from Bio import SeqIO
+
+desc = "Filter a fasta file based on ."
+command = argparse.ArgumentParser(
+    prog="fasta_filter_to_accession",
+    description=desc,
+    usage="%(prog)s [options] fasta accessions",
+)
+command.add_argument(
+    "-o",
+    "--output",
+    default=sys.stdout,
+    type=argparse.FileType("w"),
+    nargs="?",
+    help="Output result to, default:stdout",
+)
+command.add_argument("fasta", type=argparse.FileType("r"), help="Fasta file to filter")
+command.add_argument(
+    "access",
+    metavar="accessions",
+    type=str,
+    nargs="+",
+    help="List of accession to extract",
+)
+
+if __name__ == "__main__":
+    """Performed job on execution script"""
+    args = command.parse_args()
+    output = args.output
+    access = set(args.access)
+    for seq in SeqIO.parse(args.fasta, "fasta"):
+        if seq.id in access:
+            SeqIO.write(seq, output, "fasta")
+            access.remove(seq.id)
+    if len(access) > 0:
+        sys.stderr.write("Accessions not found : " + str(" - ").join(access) + "\n")